Counting soft clipped bases and reads

Question

[finswimmer]

Hello,

I'm looking for a way to count the number of soft clipped bases and reads in my bam file and calculate their fraction. What's the best way to do it?

Thanks a lot.

fin swimmer

Answer 1

[Pierre Lindenbaum]

using bioalcidaejdk : http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

and the following code

final long counts[]=new long[4];
stream().forEach(R->{
    counts[0]++;
    if(R.getReadUnmappedFlag()) return;
    Cigar cigar = R.getCigar();
    if(cigar==null || cigar.isEmpty()) return;
    counts[1]++;
    counts[2] += cigar.getReadLength();
    counts[3] += cigar.
        getCigarElements().
        stream().
        filter(C->C.getOperator().isClipping()).
        mapToInt(C->C.getLength()).
        sum();
    });

println("NUM-READS:"+counts[0]);
println("NUM-MAPPED-READS:"+counts[1]);
println("SUM-MAPPED-READS-LENGTH:"+counts[2]);
println("SUM-CLIPPING:"+counts[3]);

usage/example:

$ java -jar dist/bioalcidaejdk.jar --nocode -f biostar.code src/test/resources/S1.bam 

NUM-READS:1998
NUM-MAPPED-READS:1998
SUM-MAPPED-READS-LENGTH:139860
SUM-CLIPPING:123

[finswimmer]

Hello Pierre,

"SUM-CLIPPING" is the sum of clipped bases? If so, how can I modify the code that I get the sum of clipped reads in addition?

fin swimmer

[Pierre Lindenbaum]

that I get the sum of clipped reads in addition?

final long counts[]=new long[5];
(...)
if(cigar.isClipped()) counts[4]++;
(...)
println("NUM-READS-CLIPPED:"+counts[4]);

[finswimmer]

Works very well.

Thanks a lot.

Answer 2

[d-cameron]

The GRIDSS package contains a picard-like tool gridss.CollectCigarMetrics which will calculate and summarise the the frequency of each CIGAR element length and operation. Your fraction can then be trivially calculated using read count, and number of reads with 0 soft clip CIGAR elements.

[finswimmer]

Nice package. Is there a way to run just CollectCigarMetrics instead of the whole CallVariants pipeline?

fin swimmer

[d-cameron]

I've designed it so every step can be run as a stand-alone program. Just run java -cp gridss.jar gridss.analysis.CollectCigarMetrics. example_pipeline.sh has an example of using CollectGridssMetrics but CollectCigarMetrics works the same way.